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Sample GSM137457 Query DataSets for GSM137457
Status Public on Jun 06, 2007
Title PriG_5%O2_Expt2_Day14_rep1
Sample type RNA
 
Channel 1
Source name PriG_5%O2_Expt2_Day14
Organism Homo sapiens
Characteristics Culture initiated from G-CSF mobilized peripheral blood CD34-positive hematopoietic stem and progenitor cell donation, male donor, age 24, Caucasian
Biomaterial provider All Cells, Berkeley, CA
Treatment protocol Cultured for 14 days
Growth protocol Cultured as described (Hevehan et al., Experimental Hematology 2000;28:267-75) with IL-3, IL-6, SCF and G-CSF in serum-containing McCoy's 5A media at pH 7.2 and 5% O2
Extracted molecule total RNA
Extraction protocol Agilent RNA isolation mini-kit
Label Cy3
Label protocol Agilent Low RNA Input Fluorescent Linear Amplification kit (v2.0) (reverse transcription with oligo-dT primers, in vitro transcription with direct incorporation of fluorescently labeled CTP analogs)
 
Channel 2
Source name Universal Reference RNA
Organism Homo sapiens
Characteristics Pooled RNA from 10 human cell lines
Biomaterial provider Stratagene
Extracted molecule total RNA
Label Cy5
Label protocol Agilent Low RNA Input Fluorescent Linear Amplification kit (v2.0) (reverse transcription with oligo-dT primers, in vitro transcription with direct incorporation of fluorescently labeled CTP analogs)
 
 
Hybridization protocol Followed Agilent 60-mer oligo microarray processing protocol v 4.1, using SSC wash protocol and forced nitrogen drying
Scan protocol Scanned using Agilent Microarray Scanner (G2565BA) at 10um resolution
Description Study of in vitro granulocyte differentiation
Data processing Agilent Feature Extraction software (v.7.2) was used to assess spot quality and extract feature intensity statistics; duplicate spots were averaged; background-subtracted data were normalized using SNNLERM (Yang et al., PNAS 2003; 100:1122-1127)
 
Submission date Sep 26, 2006
Last update date Jun 06, 2007
Contact name Eleftherios Terry Papoutsakis
E-mail(s) papoutsakis@dbi.udel.edu
Organization name University of Delaware
Department Chemical Engineering
Street address 15 Innovation Way
City Newark
State/province DE
ZIP/Postal code 19711
Country USA
 
Platform ID GPL887
Series (2)
GSE5918 Temporal expression profile of granulocytic differentiation of primary CD34+ cells cultured under 5% O2 levels
GSE5922 Temporal expression profile of granulocytic differentiation of primary CD34+ cells cultured under 5% and 20% O2 levels

Data table header descriptions
ID_REF
VALUE Normalized natural log (Ch2/Ch1). Replicate spots on array representing same 60mer were averaged prior to normalization.
CH1_MEDIAN_INT Channel 1 median intensity
CH1_MEDIAN_BKG Channel 1 median background intensity
CH1_BKG_STD_DEV Channel 1 background intensity standard deviation
CH2_MEDIAN_INT Channel 2 median intensity
CH2_MEDIAN_BKG Channel 2 median background intensity
CH2_BKG_STD_DEV Channel 2 background intensity standard deviation
CONF_DIFF_EXPR Confidence of differential expression (Ch1 vs Ch2, per method of Yang et al., PNAS 2003; 100:1122-1127 [0,1]

Data table
ID_REF VALUE CH1_MEDIAN_INT CH1_MEDIAN_BKG CH1_BKG_STD_DEV CH2_MEDIAN_INT CH2_MEDIAN_BKG CH2_BKG_STD_DEV CONF_DIFF_EXPR
1 NULL 1104 34 3.15 373 38 4.42 NULL
2 NULL 79 35 3.80 48 38 4.76 NULL
3 NULL 123 35 4.35 93 38 4.77 NULL
4 NULL 3436 35 3.81 8799 38 4.63 NULL
5 NULL 311 35 3.67 475 38 4.60 NULL
6 NULL 96 35 3.68 68 38 4.32 NULL
7 NULL 857 35 3.94 79 39 4.69 NULL
8 NULL 1042 35 3.97 1173 38 5.14 NULL
9 NULL 434 35 4.12 423 39 4.77 NULL
10 NULL 99 35 4.00 74 37 4.08 NULL
11 NULL 127 35 4.21 101 39 4.32 NULL
12 NULL 158 35 4.23 140 39 4.83 NULL
13 0.0481 110 35 4.08 86 38 4.81 0.0917
14 NULL 853 36 4.27 88 38 4.87 NULL
15 0.1966 1366 37 4.32 2069 39 4.63 0.2752
16 0.0049 242 36 4.18 237 38 4.51 0.0073
17 0.1292 89 36 3.95 65 39 5.04 0.2970
18 -0.4780 497 36 4.40 353 38 4.78 0.6120
20 NULL 94 36 3.85 53 38 4.48 NULL
21 NULL 916 37 3.81 84 38 4.99 NULL

Total number of rows: 22153

Table truncated, full table size 948 Kbytes.




Supplementary data files not provided

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